Former Australian Tax Office (ATO) deputy commissioner Michael Cranston has been found not guilty of misusing his position to benefit his son.

Key points:

Mr Cranston had a 40-year career with the ATO

Outside court his wife said the charges were "based on a lot of inferences and speculation"

Mr Cranston said the accusations were among the "worst things that's ever happened in my life"

An emotional Mr Cranston fought back tears in the dock and hugged supporters when the verdict was handed down at Sydney's Downing Centre court complex.

During a three-week NSW District Court trial, a jury heard allegations Mr Cranston attempted to set up a meeting between the ATO and payroll company Plutus in 2017, which his son was involved with.

The company's accounts were frozen by the tax office due to alleged unpaid taxes and charges of about $40 million.

"I knew I hadn't done anything wrong and I'm just so happy the justice system prevailed," Mr Cranston said outside court.

"I've never felt like that in my life and I've never been so emotional in my life, I think, except for when my children were born."

"Just to actually be charged on something like this it was a shock and it's probably one of the worst things that's ever happened in my life."

Mr Cranston laughed when asked if he would be seeking to get his old job back, but revealed he would pursue consultancy work to continue his passion of working for taxpayers.

District Court Judge Robyn Tupman told Mr Cranston she found his case a "refreshing intellectual challenge" from the usual "disgusting" matters she presides over.

The judge told him he was free to leave the dock unless he found it "gorgeous".

'He should never have had to go through this'

The jury took just over two days to reach its not guilty verdict.

Last month, the court was played video of an interview between Mr Cranston and Australian Federal Police (AFP) officers on the day he was issued a court attendance notice in May 2017.

In the footage, he declared he had "nothing to hide" and was trying to "help the tax office".

Outside court, Mr Cranston's wife Gloria said the trial had taken a toll on the family.

"He should never have had to go through this," she said.

"It was based on a lot of inferences and speculation."

Mr Cranston, 59, had a glittering 40-year career with the ATO.

During the trial, the Crown alleged that between April and May of 2017, Mr Cranston told an employee to contact the audit team handling the Plutus matter, following a request for assistance from his son.

Mr Cranston told the court his son Adam came to see him in January 2017 and showed him a strongly worded letter the ATO had sent his business associate Simon Anquetil.

"I was concerned because it's the first time my son raised anything with me to do with taxation and I was grappling with the conflict question," he said.